1) For my C>T mutation at chromosome 4:152297391 it all seem to work fine.

bam-readcount -w 1 -b 20 -q 1 -f /mnt/storage/ref_fasta/Mus_musculus.GRCm38.dna.primary_assembly.fa 4T1_0Gy_0624.Aligned.sortedByCoord.out.bam 4:152297391-152297391
Minimum mapping quality is set to 1
WARNING: In read ST-K00128:117:HG5FKBBXX:6:1124:3336:48843: Couldn't find single-end mapping quality. Check to see if the SM tag is in BAM.
The previous warning has been emitted 1 times and will be disabled.
WARNING: In read ST-K00128:117:HG5FKBBXX:6:1124:3336:48843: Couldn't find number of mismatches. Check to see if the NM tag is in BAM.
The previous warning has been emitted 1 times and will be disabled.
4 152297391 G 7 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 G:7:255.00:39.71:0.00:4:3:0.35:0.00:11.71:4:0.39:100.43:0.54 T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00

2) This is a location that I have 0 reads for in my RNA seq file (chr4:147058427, A>G):

How come i sometimes get 0 reads and sometimes empty output? I want to make sure that when I have a NA output, I really do not have any reads for this location? Is this a problem with my reference fasta file?

Perhaps I missunderstand you when you say bam-readcount will return nothing for sites that do not pass my filtering criteria. How about this site? No reads here match my filtering criteria, but I still get 0s: